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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2023-05-10, 22:33 CEST based on data in:

        General Statistics

        Showing 344/344 rows and 3/6 columns.
        Sample Name% Dups% GCM Seqs
        SAMN02333917_1
        10.0%
        46%
        50.5
        SAMN02333917_2
        9.3%
        46%
        50.5
        SAMN02333918_1
        17.8%
        44%
        51.7
        SAMN02333918_2
        17.0%
        45%
        51.7
        SAMN02333919_1
        13.5%
        47%
        59.5
        SAMN02333919_2
        12.8%
        47%
        59.5
        SAMN02333920_1
        7.8%
        47%
        56.3
        SAMN02333920_2
        7.2%
        47%
        56.3
        SAMN02333921_1
        14.8%
        45%
        62.5
        SAMN02333921_2
        13.9%
        45%
        62.5
        SAMN02333922_1
        8.7%
        47%
        51.3
        SAMN02333922_2
        7.7%
        47%
        51.3
        SAMN02333923_1
        7.1%
        49%
        49.5
        SAMN02333923_2
        6.9%
        49%
        49.5
        SAMN02333924_1
        16.4%
        45%
        54.8
        SAMN02333924_2
        15.4%
        46%
        54.8
        SAMN02333925_1
        15.5%
        46%
        58.9
        SAMN02333925_2
        14.8%
        46%
        58.9
        SAMN02333926_1
        15.3%
        46%
        60.6
        SAMN02333926_2
        14.5%
        46%
        60.6
        SAMN02333936_1
        21.1%
        46%
        52.5
        SAMN02333936_2
        19.8%
        46%
        52.5
        SAMN02333939_1
        15.0%
        47%
        63.2
        SAMN02333939_2
        13.7%
        48%
        63.2
        SAMN02333940_1
        11.5%
        46%
        51.4
        SAMN02333940_2
        10.7%
        47%
        51.4
        SAMN02333941_1
        16.3%
        46%
        52.8
        SAMN02333941_2
        15.2%
        46%
        52.8
        SAMN02333942_1
        12.9%
        45%
        64.5
        SAMN02333942_2
        12.3%
        45%
        64.5
        SAMN02333943_1
        17.6%
        46%
        65.2
        SAMN02333943_2
        16.5%
        47%
        65.2
        SAMN02333944_1
        24.9%
        45%
        53.9
        SAMN02333944_2
        23.4%
        46%
        53.9
        SAMN02333945_1
        36.9%
        46%
        56.9
        SAMN02333945_2
        35.4%
        46%
        56.9
        SAMN02333946_1
        8.4%
        46%
        56.3
        SAMN02333946_2
        8.3%
        46%
        56.3
        SAMN02333947_1
        18.8%
        44%
        55.5
        SAMN02333947_2
        17.6%
        44%
        55.5
        SAMN02333948_1
        16.4%
        45%
        52.8
        SAMN02333948_2
        15.4%
        45%
        52.8
        SAMN02333956_1
        29.7%
        44%
        64.7
        SAMN02333956_2
        27.5%
        44%
        64.7
        SAMN02333957_1
        17.8%
        45%
        54.5
        SAMN02333957_2
        14.5%
        46%
        54.5
        SAMN02333958_1
        14.2%
        46%
        48.2
        SAMN02333958_2
        13.0%
        46%
        48.2
        SAMN02333960_1
        9.4%
        46%
        44.6
        SAMN02333960_2
        8.7%
        47%
        44.6
        SAMN02333961_1
        26.1%
        45%
        51.2
        SAMN02333961_2
        24.3%
        45%
        51.2
        SAMN02333962_1
        28.7%
        47%
        58.9
        SAMN02333962_2
        26.8%
        47%
        58.9
        SAMN02333963_1
        21.7%
        44%
        58.7
        SAMN02333963_2
        19.8%
        45%
        58.7
        SAMN02333964_1
        18.5%
        46%
        50.8
        SAMN02333964_2
        16.6%
        46%
        50.8
        SAMN02333965_1
        14.4%
        45%
        61.8
        SAMN02333965_2
        13.4%
        46%
        61.8
        SAMN02333966_1
        12.4%
        47%
        56.0
        SAMN02333966_2
        11.8%
        47%
        56.0
        SAMN02333967_1
        11.1%
        45%
        56.6
        SAMN02333967_2
        10.6%
        45%
        56.6
        SAMN02333968_1
        16.1%
        46%
        54.6
        SAMN02333968_2
        15.3%
        46%
        54.6
        SAMN02333969_1
        15.6%
        44%
        50.9
        SAMN02333969_2
        14.7%
        44%
        50.9
        SAMN02333970_1
        19.6%
        47%
        114.0
        SAMN02333970_2
        18.2%
        47%
        114.0
        SAMN02333977_1
        34.1%
        45%
        57.9
        SAMN02333977_2
        32.4%
        45%
        57.9
        SAMN02333978_1
        13.9%
        46%
        64.3
        SAMN02333978_2
        12.8%
        46%
        64.3
        SAMN02333979_1
        11.7%
        47%
        62.7
        SAMN02333979_2
        10.9%
        47%
        62.7
        SAMN02333980_1
        19.4%
        45%
        58.7
        SAMN02333980_2
        17.7%
        45%
        58.7
        SAMN02333981_1
        15.7%
        46%
        62.2
        SAMN02333981_2
        14.9%
        46%
        62.2
        SAMN02333982_1
        17.0%
        46%
        57.4
        SAMN02333982_2
        15.2%
        46%
        57.4
        SAMN02333983_1
        19.1%
        46%
        56.0
        SAMN02333983_2
        17.6%
        46%
        56.0
        SAMN02333984_1
        12.2%
        44%
        51.9
        SAMN02333984_2
        11.5%
        45%
        51.9
        SAMN02333985_1
        23.5%
        46%
        59.1
        SAMN02333985_2
        22.0%
        46%
        59.1
        SAMN02333986_1
        16.6%
        45%
        53.0
        SAMN02333986_2
        15.6%
        45%
        53.0
        SAMN02333993_1
        17.1%
        45%
        46.8
        SAMN02333993_2
        16.1%
        46%
        46.8
        SAMN02333994_1
        23.6%
        45%
        53.9
        SAMN02333994_2
        22.1%
        45%
        53.9
        SAMN02333996_1
        17.1%
        46%
        47.5
        SAMN02333996_2
        12.8%
        47%
        47.5
        SAMN02333997_1
        14.6%
        48%
        59.3
        SAMN02333997_2
        13.1%
        49%
        59.3
        SAMN02333998_1
        26.2%
        45%
        53.6
        SAMN02333998_2
        24.7%
        45%
        53.6
        SAMN02333999_1
        12.2%
        45%
        47.5
        SAMN02333999_2
        10.9%
        45%
        47.5
        SAMN02334000_1
        13.9%
        47%
        57.6
        SAMN02334000_2
        13.1%
        47%
        57.6
        SAMN02334001_1
        21.3%
        47%
        57.8
        SAMN02334001_2
        19.4%
        47%
        57.8
        SAMN02334002_1
        14.9%
        45%
        53.7
        SAMN02334002_2
        13.8%
        45%
        53.7
        SAMN02334003_1
        29.2%
        44%
        58.5
        SAMN02334003_2
        27.6%
        44%
        58.5
        SAMN02334004_1
        12.5%
        45%
        55.1
        SAMN02334004_2
        11.3%
        45%
        55.1
        SAMN02334005_1
        18.5%
        48%
        47.2
        SAMN02334005_2
        17.4%
        48%
        47.2
        SAMN02334006_1
        20.6%
        45%
        52.6
        SAMN02334006_2
        19.2%
        45%
        52.6
        SAMN02334016_1
        17.5%
        47%
        55.2
        SAMN02334016_2
        16.2%
        47%
        55.2
        SAMN02334017_1
        10.0%
        46%
        63.4
        SAMN02334017_2
        9.0%
        46%
        63.4
        SAMN02334018_1
        21.2%
        45%
        58.9
        SAMN02334018_2
        20.0%
        45%
        58.9
        SAMN02334019_1
        19.2%
        45%
        60.6
        SAMN02334019_2
        18.2%
        46%
        60.6
        SAMN02334021_1
        9.2%
        48%
        58.8
        SAMN02334021_2
        8.5%
        48%
        58.8
        SAMN02334022_1
        16.4%
        46%
        64.5
        SAMN02334022_2
        15.6%
        46%
        64.5
        SAMN02334023_1
        12.3%
        45%
        52.0
        SAMN02334023_2
        11.3%
        45%
        52.0
        SAMN02334024_1
        16.0%
        45%
        53.1
        SAMN02334024_2
        14.3%
        45%
        53.1
        SAMN02334025_1
        14.0%
        45%
        55.9
        SAMN02334025_2
        12.8%
        45%
        55.9
        SAMN02334026_1
        12.8%
        45%
        49.9
        SAMN02334026_2
        12.1%
        45%
        49.9
        SAMN02334027_1
        12.1%
        46%
        49.2
        SAMN02334027_2
        11.1%
        46%
        49.2
        SAMN02334028_1
        20.6%
        46%
        55.0
        SAMN02334028_2
        19.6%
        46%
        55.0
        SAMN02334030_1
        14.7%
        46%
        46.2
        SAMN02334030_2
        13.9%
        47%
        46.2
        SAMN02334031_1
        10.2%
        46%
        10.7
        SAMN02334031_2
        8.6%
        46%
        10.7
        SAMN02334036_1
        9.9%
        47%
        59.6
        SAMN02334036_2
        9.4%
        47%
        59.6
        SAMN02334037_1
        15.8%
        47%
        63.0
        SAMN02334037_2
        14.3%
        47%
        63.0
        SAMN02334038_1
        20.7%
        45%
        61.7
        SAMN02334038_2
        19.4%
        45%
        61.7
        SAMN02334039_1
        14.5%
        44%
        55.8
        SAMN02334039_2
        13.8%
        44%
        55.8
        SAMN02334040_1
        12.4%
        47%
        50.5
        SAMN02334040_2
        11.4%
        47%
        50.5
        SAMN02334041_1
        12.1%
        45%
        47.5
        SAMN02334041_2
        10.9%
        45%
        47.5
        SAMN02334042_1
        20.8%
        45%
        58.8
        SAMN02334042_2
        19.2%
        45%
        58.8
        SAMN02334043_1
        11.6%
        47%
        51.8
        SAMN02334043_2
        10.5%
        47%
        51.8
        SAMN02334049_1
        35.9%
        45%
        63.9
        SAMN02334049_2
        33.8%
        45%
        63.9
        SAMN02334051_1
        12.6%
        47%
        48.2
        SAMN02334051_2
        11.6%
        47%
        48.2
        SAMN02334052_1
        25.9%
        45%
        48.1
        SAMN02334052_2
        24.1%
        45%
        48.1
        SAMN02334053_1
        23.6%
        45%
        57.0
        SAMN02334053_2
        21.5%
        45%
        57.0
        SAMN02334054_1
        10.8%
        47%
        51.2
        SAMN02334054_2
        9.9%
        47%
        51.2
        SAMN02334055_1
        13.4%
        46%
        52.3
        SAMN02334055_2
        12.8%
        46%
        52.3
        SAMN02334056_1
        14.2%
        46%
        47.5
        SAMN02334056_2
        13.6%
        46%
        47.5
        SAMN02334057_1
        23.3%
        44%
        66.0
        SAMN02334057_2
        21.4%
        45%
        66.0
        SAMN02334058_1
        31.0%
        46%
        76.8
        SAMN02334058_2
        28.7%
        46%
        76.8
        SAMN02334059_1
        14.0%
        45%
        61.3
        SAMN02334059_2
        12.8%
        45%
        61.3
        SAMN02334060_1
        23.7%
        45%
        50.9
        SAMN02334060_2
        22.3%
        45%
        50.9
        SAMN02334065_1
        15.0%
        45%
        54.9
        SAMN02334065_2
        14.3%
        45%
        54.9
        SAMN02334066_1
        14.8%
        46%
        47.3
        SAMN02334066_2
        13.5%
        46%
        47.3
        SAMN02334067_1
        12.0%
        44%
        52.8
        SAMN02334067_2
        11.4%
        44%
        52.8
        SAMN02334068_1
        19.6%
        45%
        52.0
        SAMN02334068_2
        18.2%
        45%
        52.0
        SAMN02334069_1
        18.5%
        46%
        55.0
        SAMN02334069_2
        17.8%
        46%
        55.0
        SAMN02334070_1
        27.6%
        46%
        112.9
        SAMN02334070_2
        18.7%
        46%
        112.9
        SAMN02334072_1
        17.1%
        45%
        48.0
        SAMN02334072_2
        16.2%
        45%
        48.0
        SAMN02334073_1
        14.5%
        45%
        52.8
        SAMN02334073_2
        13.8%
        45%
        52.8
        SAMN02334074_1
        12.4%
        47%
        44.6
        SAMN02334074_2
        11.7%
        47%
        44.6
        SAMN02334075_1
        25.2%
        46%
        50.7
        SAMN02334075_2
        22.0%
        46%
        50.7
        SAMN02334076_1
        23.6%
        43%
        53.0
        SAMN02334076_2
        22.8%
        43%
        53.0
        SAMN02334077_1
        24.8%
        44%
        103.3
        SAMN02334077_2
        20.4%
        45%
        103.3
        SAMN02334078_1
        19.6%
        46%
        52.1
        SAMN02334078_2
        18.2%
        46%
        52.1
        SAMN02334079_1
        24.2%
        46%
        63.4
        SAMN02334079_2
        23.1%
        46%
        63.4
        SAMN02334080_1
        14.6%
        46%
        61.6
        SAMN02334080_2
        13.9%
        46%
        61.6
        SAMN02334081_1
        26.6%
        46%
        48.5
        SAMN02334081_2
        25.1%
        46%
        48.5
        SAMN02334082_1
        16.8%
        45%
        53.3
        SAMN02334082_2
        16.0%
        45%
        53.3
        SAMN02334083_1
        15.9%
        45%
        47.7
        SAMN02334083_2
        14.6%
        45%
        47.7
        SAMN02334084_1
        25.3%
        46%
        51.5
        SAMN02334084_2
        23.2%
        46%
        51.5
        SAMN02334086_1
        30.0%
        46%
        53.4
        SAMN02334086_2
        27.5%
        46%
        53.4
        SAMN02334087_1
        22.5%
        44%
        50.7
        SAMN02334087_2
        21.6%
        45%
        50.7
        SAMN02334088_1
        15.1%
        44%
        51.0
        SAMN02334088_2
        12.1%
        44%
        51.0
        SAMN02334089_1
        17.9%
        44%
        54.6
        SAMN02334089_2
        16.6%
        45%
        54.6
        SAMN02334090_1
        12.9%
        45%
        46.6
        SAMN02334090_2
        12.0%
        45%
        46.6
        SAMN02334091_1
        15.9%
        46%
        54.9
        SAMN02334091_2
        14.2%
        46%
        54.9
        SAMN02334092_1
        28.6%
        45%
        42.8
        SAMN02334092_2
        25.4%
        45%
        42.8
        SAMN02334093_1
        13.1%
        47%
        55.4
        SAMN02334093_2
        12.0%
        47%
        55.4
        SAMN02334094_1
        30.0%
        45%
        50.7
        SAMN02334094_2
        28.7%
        45%
        50.7
        SAMN02334095_1
        13.5%
        50%
        52.3
        SAMN02334095_2
        12.6%
        50%
        52.3
        SAMN02334096_1
        19.7%
        44%
        51.0
        SAMN02334096_2
        18.4%
        44%
        51.0
        SAMN02334097_1
        16.9%
        44%
        47.2
        SAMN02334097_2
        16.0%
        44%
        47.2
        SAMN02334098_1
        19.2%
        44%
        47.3
        SAMN02334098_2
        18.4%
        44%
        47.3
        SAMN02334099_1
        20.0%
        46%
        47.6
        SAMN02334099_2
        19.2%
        46%
        47.6
        SAMN02334101_1
        21.1%
        45%
        47.9
        SAMN02334101_2
        19.9%
        45%
        47.9
        SAMN02334102_1
        13.5%
        44%
        55.8
        SAMN02334102_2
        12.6%
        45%
        55.8
        SAMN02334103_1
        17.8%
        45%
        58.6
        SAMN02334103_2
        17.2%
        46%
        58.6
        SAMN02334104_1
        31.2%
        45%
        36.6
        SAMN02334104_2
        20.1%
        45%
        36.6
        SAMN02334105_1
        47.2%
        45%
        60.2
        SAMN02334105_2
        45.3%
        45%
        60.2
        SAMN02334106_1
        28.8%
        45%
        61.9
        SAMN02334106_2
        27.5%
        45%
        61.9
        SAMN02334108_1
        13.5%
        44%
        48.6
        SAMN02334108_2
        12.8%
        44%
        48.6
        SAMN02334109_1
        18.9%
        46%
        56.3
        SAMN02334109_2
        17.5%
        47%
        56.3
        SAMN02334110_1
        31.0%
        46%
        54.5
        SAMN02334110_2
        27.1%
        46%
        54.5
        SAMN02334111_1
        12.0%
        47%
        45.3
        SAMN02334111_2
        10.9%
        47%
        45.3
        SAMN02334112_1
        16.0%
        51%
        47.3
        SAMN02334112_2
        15.1%
        51%
        47.3
        SAMN02334113_1
        17.3%
        45%
        49.6
        SAMN02334113_2
        15.2%
        45%
        49.6
        SAMN02334114_1
        20.5%
        46%
        54.8
        SAMN02334114_2
        19.4%
        46%
        54.8
        SAMN02334116_1
        23.0%
        45%
        56.4
        SAMN02334116_2
        21.6%
        45%
        56.4
        SAMN02334117_1
        23.4%
        46%
        54.0
        SAMN02334117_2
        21.4%
        46%
        54.0
        SAMN02334118_1
        26.8%
        45%
        107.3
        SAMN02334118_2
        22.3%
        45%
        107.3
        SAMN02334119_1
        16.6%
        45%
        48.2
        SAMN02334119_2
        15.8%
        46%
        48.2
        SAMN02334120_1
        24.1%
        45%
        50.1
        SAMN02334120_2
        23.3%
        45%
        50.1
        SAMN02334121_1
        26.6%
        45%
        53.5
        SAMN02334121_2
        25.4%
        45%
        53.5
        SAMN02334122_1
        25.5%
        45%
        57.2
        SAMN02334122_2
        24.3%
        45%
        57.2
        SAMN02334123_1
        18.0%
        44%
        52.3
        SAMN02334123_2
        17.0%
        45%
        52.3
        SAMN02334124_1
        16.1%
        47%
        57.1
        SAMN02334124_2
        14.8%
        47%
        57.1
        SAMN02334125_1
        16.8%
        45%
        39.9
        SAMN02334125_2
        11.8%
        45%
        39.9
        SAMN02334126_1
        15.1%
        47%
        46.7
        SAMN02334126_2
        14.3%
        47%
        46.7
        SAMN02334127_1
        13.1%
        47%
        48.7
        SAMN02334127_2
        12.5%
        47%
        48.7
        SAMN02334128_1
        18.7%
        44%
        53.4
        SAMN02334128_2
        17.7%
        45%
        53.4
        SAMN02334130_1
        32.8%
        45%
        99.9
        SAMN02334130_2
        27.7%
        45%
        99.9
        SAMN02334132_1
        10.0%
        47%
        45.3
        SAMN02334132_2
        9.4%
        47%
        45.3
        SAMN02334133_1
        15.2%
        46%
        50.5
        SAMN02334133_2
        14.4%
        46%
        50.5
        SAMN02334134_1
        16.9%
        45%
        47.0
        SAMN02334134_2
        15.7%
        46%
        47.0
        SAMN02334135_1
        18.3%
        45%
        43.5
        SAMN02334135_2
        17.6%
        45%
        43.5
        SAMN02334136_1
        19.7%
        45%
        51.8
        SAMN02334136_2
        18.6%
        46%
        51.8
        SAMN02334137_1
        18.8%
        46%
        52.6
        SAMN02334137_2
        17.5%
        46%
        52.6
        SAMN02334138_1
        15.6%
        45%
        43.5
        SAMN02334138_2
        15.1%
        45%
        43.5
        SAMN02334139_1
        17.5%
        46%
        54.7
        SAMN02334139_2
        16.7%
        46%
        54.7
        SAMN02334140_1
        17.7%
        44%
        39.5
        SAMN02334140_2
        12.3%
        44%
        39.5
        SAMN02334142_1
        22.1%
        45%
        105.2
        SAMN02334142_2
        17.3%
        46%
        105.2
        SAMN02334143_1
        10.0%
        49%
        49.0
        SAMN02334143_2
        9.1%
        49%
        49.0
        SAMN02334144_1
        21.3%
        45%
        50.2
        SAMN02334144_2
        19.7%
        45%
        50.2
        SAMN02334145_1
        24.0%
        46%
        49.2
        SAMN02334145_2
        22.6%
        46%
        49.2
        SAMN02334146_1
        15.5%
        45%
        56.6
        SAMN02334146_2
        13.7%
        45%
        56.6
        SAMN02334147_1
        18.6%
        46%
        48.3
        SAMN02334147_2
        17.8%
        46%
        48.3
        SAMN02334148_1
        31.8%
        46%
        46.7
        SAMN02334148_2
        30.7%
        46%
        46.7
        SAMN02334149_1
        29.5%
        45%
        63.6
        SAMN02334149_2
        26.7%
        45%
        63.6
        SAMN02334150_1
        16.4%
        46%
        50.0
        SAMN02334150_2
        15.0%
        46%
        50.0
        SAMN02334151_1
        27.5%
        44%
        54.3
        SAMN02334151_2
        26.1%
        44%
        54.3
        SAMN02334152_1
        67.7%
        45%
        41.1
        SAMN02334152_2
        12.6%
        48%
        41.1
        SAMN02334153_1
        13.3%
        46%
        48.8
        SAMN02334153_2
        12.7%
        46%
        48.8

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

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        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

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        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

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        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

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        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

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        Sequence Length Distribution

        All samples have sequences of a single length (101bp).

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

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        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

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        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

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        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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        MultiQC v1.14 - Written by Phil Ewels, available on GitHub.

        This report uses HighCharts, jQuery, jQuery UI, Bootstrap, FileSaver.js and clipboard.js.